--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: lncRNA Expression - P.generosa lncRNA Expression Using StringTie date: '2023-05-04 12:19' tags: - jupyter - lncRNA - Panopea generosa - Pacific geoduck - stringtie categories: - 2023 - Miscellaneous --- After [identifying lncRNA in _P.generosa_](https://robertslab.github.io/sams-notebook/posts/2023/2023-05-02-lncRNA-Identification---P.generosa-lncRNAs-using-CPC2-and-bedtools/), [Steven asked that I generate an tissue-specific expression/count matrix](https://github.com/RobertsLab/resources/issues/1642) (GitHub Issue). Looking through the documentation for [`StringTie`](https://ccb.jhu.edu/software/stringtie/), I decided that [`StringTie`](https://ccb.jhu.edu/software/stringtie/) would work for this. The overall approach: - Use tissue-specifc BAMs [from HISAT2 alignments](https://robertslab.github.io/sams-notebook/posts/2023/2023-04-26-Transcript-Alignments---P.generosa-RNA-seq-Alignments-for-lncRNA-Identification-Using-Hisat2-StingTie-and-gffcompare-on-Mox/) - Use ["canonical" lncRNA GTF representing all lncRNAs found across all tissues](https://robertslab.github.io/sams-notebook/posts/2023/2023-05-02-lncRNA-Identification---P.generosa-lncRNAs-using-CPC2-and-bedtools/) as input to [`StringTie`](https://ccb.jhu.edu/software/stringtie/). - Use [`StringTie`](https://ccb.jhu.edu/software/stringtie/)'s expression estimation feature to generate read coverage and expression (FPKM) for each lncRNA. - Use [`StringTie`](https://ccb.jhu.edu/software/stringtie/)'s Python script (`prepDE.py3`) to generate tissue/sample-specific count matrix. This was all run on Raven, using a Jupyter Notebook. Links below: - [20230504-pgen-lncRNA-expression.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20230504-pgen-lncRNA-expression.ipynb) Jupyter Notebook (NB Viewer): - [20230502-pgen-lncRNA-identification.ipynb](https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230504-pgen-lncRNA-expression.ipynb) --- # RESULTS This produced `ballgown` expression files, as well as a transcript read count matrix with a column for each tissue/sample. I'm only linking directly to the final matrix file due to the number of samples and redundant `ballgown` files/structure. To view the organization of the output directory, see the [directory tree below](#directory-tree) Output folder: - [20230504-pgen-lncRNA-expression/](https://gannet.fish.washington.edu/Atumefaciens/20230504-pgen-lncRNA-expression/) #### Transcript count matrix (CSV) - [`20230504-pgen-lncRNA-expression/transcript_count_matrix.csv`](https://gannet.fish.washington.edu/Atumefaciens/20230504-pgen-lncRNA-expression/transcript_count_matrix.csv) | transcript_id | ctenidia | gonad | heart | juvenile | larvae | |---------------|----------|-------|-------|----------|--------| | MSTRG.1.1 | 34 | 16 | 13 | 93 | 6 | | MSTRG.2.1 | 18 | 5 | 2 | 9 | 2 | | MSTRG.3.1 | 15 | 9 | 48 | 171 | 60 | | MSTRG.22.1 | 4 | 24 | 7 | 27 | 22 | | MSTRG.9.1 | 3 | 133 | 1 | 1681 | 245 | | MSTRG.11.1 | 88 | 123 | 77 | 144 | 95 | | MSTRG.12.1 | 3 | 81 | 12 | 47 | 50 | | MSTRG.25.1 | 6 | 47 | 8 | 0 | 1 | | MSTRG.27.1 | 4 | 79 | 9 | 12 | 4 | ### Directory tree ``` ├── [4.0K] ctenidia │   ├── [3.9M] ctenidia-pgen-lncRNA-stringtie.gtf │   ├── [137K] e2t.ctab │   ├── [997K] e_data.ctab │   ├── [ 10] i2t.ctab │   ├── [ 48] i_data.ctab │   └── [1.2M] t_data.ctab ├── [316K] gene_count_matrix.csv ├── [4.0K] gonad │   ├── [137K] e2t.ctab │   ├── [1002K] e_data.ctab │   ├── [3.9M] gonad-pgen-lncRNA-stringtie.gtf │   ├── [ 10] i2t.ctab │   ├── [ 48] i_data.ctab │   └── [1.2M] t_data.ctab ├── [4.0K] heart │   ├── [137K] e2t.ctab │   ├── [990K] e_data.ctab │   ├── [3.9M] heart-pgen-lncRNA-stringtie.gtf │   ├── [ 10] i2t.ctab │   ├── [ 48] i_data.ctab │   └── [1.2M] t_data.ctab ├── [4.0K] juvenile │   ├── [137K] e2t.ctab │   ├── [1.0M] e_data.ctab │   ├── [ 10] i2t.ctab │   ├── [ 48] i_data.ctab │   ├── [3.9M] juvenile-pgen-lncRNA-stringtie.gtf │   └── [1.2M] t_data.ctab ├── [4.0K] larvae │   ├── [137K] e2t.ctab │   ├── [1001K] e_data.ctab │   ├── [ 10] i2t.ctab │   ├── [ 48] i_data.ctab │   ├── [3.9M] larvae-pgen-lncRNA-stringtie.gtf │   └── [1.2M] t_data.ctab └── [409K] transcript_count_matrix.csv 5 directories, 32 files ```